This protocol is a phase III, double-blind, randomized, baseline-controlled, two-treatment crossover study to separately evaluate the effects of pantoprazole 40 mg and omeprazole 20 mg on intragastric and intraesophageal pH profiles in patients with gastroesophageal reflux disease (GERD). Patients undergo a screening endoscopy, manometry and pH measurement. Eligible patients receive one of two study drugs for 8 days separated by at least a 10-day washout period before receiving the other study medication. In addition to a 24-hour overnight stay for baseline pH measurement, each treatment period requires two overnight stays for 24-hour dual intragastric and intraesophageal pH measurement. Each patient will participate in the study for approximately 6.5 (up to 8) weeks. With this study, therefore, the investigator will measure the extent of suppression of gastric acid secretion on day 1 (onset) and day 8 of treatment for each medication. Information about GERD symptomatology will also be collected.